The interaction of substituted 2-phenylquinoline intercalators with poly(A).poly(U): classical and threading intercalation modes with RNA

Biopolymers. 1994 Jan;34(1):61-73. doi: 10.1002/bip.360340108.

Abstract

The interaction of a series of 2-phenylquinoline derivatives with RNA was investigated by means of viscometric, pKa, spectroscopic, binding, Tm, and kinetic methods. Compounds 1, 2, and 3 have a piperazyl substituent at the para, meta, or ortho position, respectively, while 4 has an unsubstituted phenyl ring. The pKa results suggest that 1 has three charges, 2 and 3 have more than two charges, and 4 has two charges at pH 6.2. Spectroscopic and Tm results indicate that 1 binds more strongly to RNA than 2-4. Kinetic and modeling results indicate that 1 is a threading intercalator while 2 and 4 are classical intercalators. All experimental results indicate that 3, which has a large twist between the phenyl and quinoline rings, binds weakly with RNA.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Antiviral Agents / chemistry
  • Antiviral Agents / pharmacology
  • Binding Sites
  • HIV-1 / drug effects
  • Intercalating Agents / chemistry*
  • Intercalating Agents / pharmacology
  • Kinetics
  • Poly A-U / chemistry*
  • Quinolines / chemistry
  • Quinolines / pharmacology
  • RNA / chemistry*
  • RNA / drug effects
  • RNA, Viral / chemistry
  • RNA, Viral / drug effects

Substances

  • Antiviral Agents
  • Intercalating Agents
  • Quinolines
  • RNA, Viral
  • Poly A-U
  • RNA